> For the complete documentation index, see [llms.txt](https://bridge-lab.gitbook.io/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://bridge-lab.gitbook.io/docs/imaging/image-analysis/segmentation/nomis.md).

# NOMIS

<mark style="color:yellow;">**NOTE**</mark>: NOMIS requires Freesurfer 6.0 outputs. For more detail see [Freesurfer](/docs/imaging/image-analysis/segmentation/freesurfer.md).

To derive norm scores from Freesurfer 5.3, see the document below.

{% file src="/files/KjIB1iyXijJWbcQkPFfe" %}

## Downloading NOMIS

{% embed url="<https://github.com/medicslaboratory/NOMIS>" %}

Download NOMIS from the github link above

## Setting up a NOMIS conda environment

create a conda environment:

```bash
conda create -n "nomis" python==3.7.4
```

install dependencies

<pre class="language-bash"><code class="lang-bash"><strong>conda activate nomis
</strong><strong>pip install argparse==1.1
</strong>pip install nibabel==2.5.1
pip install numpy==1.17.2
pip install pandas==0.25.1
pip install pickle4
pip install scikit-learn==0.21.3
</code></pre>

## Running NOMIS

For an automated script to run NOMIS on your BIDS formatted and recon-all'd data, see: <https://github.com/ryn-thorn/Image_Analysis_Scripts/tree/main/NOMIS>

{% embed url="<https://github.com/ryn-thorn/Image_Analysis_Scripts/tree/main/NOMIS>" %}

Create a setup file. This is a .csv file with five columns: id, age, sex, manufacturer, and mfs.

* id: subject ID as it appears on in Freesurfer outputs
* age: can be a whole number or a decimal
* sex: M or F, uncertain of how this should be marked for people who identify as a gender they were not assigned at birth
* manufacturer: manufacturer of the MRI machine (for our purposes, usually Seimens)
* mfs: manufacturer field strength (for our purposes, usually 3)

See example below:

{% file src="/files/h9eez2QVp6k9JpmUPlOf" %}

Run NOMIS using the following command structure:

```
conda activate nomis
python [path to nomis folder]/nomis.py -csv [path to setup file] -s [path to FS outputs] -o [path to nomis outputs]
```

## NOMIS Outputs

<figure><img src="/files/xQm3voWyWqctGHrJHxWr" alt=""><figcaption></figcaption></figure>